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- PDB-3zqc: Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bo... -

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Basic information

Entry
Database: PDB / ID: 3zqc
TitleStructure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal beta-hairpin conformation
Components
  • (MRE-1) x 2
  • MYB3
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / DNA-BINDING PROTEIN / NUCLEUS
Function / homology
Function and homology information


transcription coregulator activity / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / MYB3
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWei, S.-Y. / Lou, Y.-C. / Tsai, J.-Y. / Hsu, H.-M. / Tai, J.-H. / Hsiao, C.-D. / Chen, C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structure of the Trichomonas Vaginalis Myb3 DNA-Binding Domain Bound to a Promoter Sequence Reveals a Unique C-Terminal Beta-Hairpin Conformation.
Authors: Wei, S.-Y. / Lou, Y.-C. / Tsai, J.-Y. / Ho, M.R. / Chou, C.C. / Rajasekaran, M. / Hsu, H.-M. / Tai, J.-H. / Hsiao, C.-D. / Chen, C.
History
DepositionJun 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYB3
B: MRE-1
C: MRE-1
D: MYB3
E: MRE-1
F: MRE-1
G: MYB3
H: MRE-1
I: MRE-1
J: MYB3
K: MRE-1
L: MRE-1


Theoretical massNumber of molelcules
Total (without water)100,68812
Polymers100,68812
Non-polymers00
Water1,76598
1
A: MYB3
B: MRE-1
C: MRE-1


Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-20.4 kcal/mol
Surface area11630 Å2
MethodPISA
2
D: MYB3
E: MRE-1
F: MRE-1


Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-19.1 kcal/mol
Surface area11640 Å2
MethodPISA
3
G: MYB3
H: MRE-1
I: MRE-1


Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-21.2 kcal/mol
Surface area11570 Å2
MethodPISA
4
J: MYB3
K: MRE-1
L: MRE-1


Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-20.5 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.810, 71.770, 87.820
Angle α, β, γ (deg.)94.68, 97.84, 99.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MYB3 / MYB-LIKE DNA-BINDING DOMAIN CONTAINING PROTEIN


Mass: 15380.552 Da / Num. of mol.: 4 / Fragment: DNA-BINDING DOMAIN, RESIDUES 53-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Plasmid: PET29B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2D9X4
#2: DNA chain
MRE-1


Mass: 4929.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) TRICHOMONAS VAGINALIS (eukaryote)
#3: DNA chain
MRE-1


Mass: 4862.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) TRICHOMONAS VAGINALIS (eukaryote)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 23110 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.46
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.02 / % possible all: 87.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8A

1h8a


Resolution: 2.9→28.7 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 258958.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 954 4.9 %RANDOM
Rwork0.218 ---
obs0.218 19482 80.8 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1-27.58 Å2-4.4 Å240.62 Å2
2---7.02 Å2-3.64 Å2
3----20.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 2600 0 98 6627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.486 120 5.4 %
Rwork0.412 2101 -
obs--55.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP

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